.Dd July 4, 2008
.Os "Open Babel" 2.2
.Dt obfit 1 URM
.Sh NAME
.Nm obfit
.Nd "superimpose two molecules based on a pattern"
.Sh SYNOPSIS
.Nm
.Ar SMARTS-pattern
.Ar fixed-file
.Ar outfile
.Sh DESCRIPTION
Superimpose two molecules using a quaternion fit. The atoms used to
fit the two molecules are defined by the SMARTS pattern given by the
user. It is useful to align congeneric series of molecules on a common
structural scaffold for 3D-QSAR studies. It can also be useful for
displaying the results of conformational generation.
.Pp
Any molecules matching the supplied SMARTS pattern will be rotated and
translated to provide the smallest possible RMSD between the matching
regions. If a molecule does not match the SMARTS pattern, it will be
output with no transformation.
.Sh EXAMPLES
Align all the molecules in 'testmv.sdf' on a single molecule of 'testref.sdf' by superimposing them on its N-methylpiperidyl portion (and outputting a new SD file to the standard output):
.Pp
.Dl "obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf"
.Sh SEE ALSO
.Xr babel 1 ,
.Xr obchiral 1 ,
.Xr obfit 1 ,
.Xr obgrep 1 ,
.Xr obrotate 1 .
.Pp
The web pages for Open Babel can be found at:
\%<\fBhttp://openbabel.org/\fR>
.Pp
A guide for constructing SMARTS patterns can be found at:
\%<\fBhttp://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR>
.Sh AUTHORS
The obfit program was contributed by
.An Fabien Fontaine
.Pp
.An -nosplit
Open Babel is developed by a cast of many, including currrent maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An Michael Banck , 
and innumerable others who have contributed fixes and additions. 
For more contributors to Open Babel, see 
\%<\fBhttp://openbabel.org/wiki/THANKS\fR>
.Sh COPYRIGHT
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 
.br
Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and
other contributors.
.Pp
 This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
.Pp
 This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
